common/clitkDicomRTStruct2ImageFilter.cxx

   1 /*=========================================================================
   2   Program:         vv http://www.creatis.insa-lyon.fr/rio/vv
   3   Main authors :   XX XX XX
   4
   5   Authors belongs to:
   6   - University of LYON           http://www.universite-lyon.fr/
   7   - Léon Bérard cancer center    http://www.centreleonberard.fr
   8   - CREATIS CNRS laboratory      http://www.creatis.insa-lyon.fr
   9
  10   This software is distributed WITHOUT ANY WARRANTY; without even
  11   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  12   PURPOSE.  See the copyright notices for more information.
  13
  14   It is distributed under dual licence
  15   - BSD       http://www.opensource.org/licenses/bsd-license.php
  16   - CeCILL-B  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17
  18   =========================================================================*/
  19
  20 #include <iterator>
  21 #include <algorithm>
  22
  23 // clitk
  24 #include "clitkDicomRTStruct2ImageFilter.h"
  25 #include "clitkImageCommon.h"
  26
  27 // vtk
  28 #include <vtkPolyDataToImageStencil.h>
  29 #include <vtkSmartPointer.h>
  30 #include <vtkImageStencil.h>
  31 #include <vtkLinearExtrusionFilter.h>
  32 #include <vtkMetaImageWriter.h>
  33
  34
  35 //--------------------------------------------------------------------
  36 clitk::DicomRTStruct2ImageFilter::DicomRTStruct2ImageFilter()
  37 {
  38   mROI = NULL;
  39   mWriteOutput = false;
  40   mCropMask = true;
  41 }
  42 //--------------------------------------------------------------------
  43
  44
  45 //--------------------------------------------------------------------
  46 clitk::DicomRTStruct2ImageFilter::~DicomRTStruct2ImageFilter()
  47 {
  48
  49 }
  50 //--------------------------------------------------------------------
  51
  52 bool clitk::DicomRTStruct2ImageFilter::ImageInfoIsSet() const
  53 {
  54   return mSize.size() && mSpacing.size() && mOrigin.size();
  55 }
  56
  57 //--------------------------------------------------------------------
  58 void clitk::DicomRTStruct2ImageFilter::SetROI(clitk::DicomRT_ROI * roi)
  59 {
  60   mROI = roi;
  61 }
  62 //--------------------------------------------------------------------
  63
  64
  65 //--------------------------------------------------------------------
  66 void clitk::DicomRTStruct2ImageFilter::SetCropMaskEnabled(bool b)
  67 {
  68   mCropMask = b;
  69 }
  70 //--------------------------------------------------------------------
  71
  72
  73 //--------------------------------------------------------------------
  74 void clitk::DicomRTStruct2ImageFilter::SetOutputImageFilename(std::string s)
  75 {
  76   mOutputFilename = s;
  77   mWriteOutput = true;
  78 }
  79 //--------------------------------------------------------------------
  80
  81
  82 //--------------------------------------------------------------------
  83 void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
  84 {
  85   itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
  86   if (header->GetNumberOfDimensions() < 3) {
  87     std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
  88     exit(0);
  89   }
  90   if (header->GetNumberOfDimensions() > 3) {
  91     std::cerr << "Warning dimension > 3 are ignored" << std::endl;
  92   }
  93   mSpacing.resize(3);
  94   mOrigin.resize(3);
  95   mSize.resize(3);
  96   for(unsigned int i=0; i<3; i++) {
  97     mSpacing[i] = header->GetSpacing(i);
  98     mOrigin[i] = header->GetOrigin(i);
  99     mSize[i] = header->GetDimensions(i);
 100   }
 101 }
 102 //--------------------------------------------------------------------
 103
 104 void clitk::DicomRTStruct2ImageFilter::SetOutputOrigin(const double* origin)
 105 {
 106   std::copy(origin,origin+3,std::back_inserter(mOrigin));
 107 }
 108 //--------------------------------------------------------------------
 109 void clitk::DicomRTStruct2ImageFilter::SetOutputSpacing(const double* spacing)
 110 {
 111   std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
 112 }
 113 //--------------------------------------------------------------------
 114 void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
 115 {
 116   std::copy(size,size+3,std::back_inserter(mSize));
 117 }
 118
 119 //--------------------------------------------------------------------
 120 void clitk::DicomRTStruct2ImageFilter::Update()
 121 {
 122   if (!mROI) {
 123     std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
 124     exit(0);
 125   }
 126   if (!ImageInfoIsSet()) {
 127     std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
 128     exit(0);
 129   }
 130
 131   // Get Mesh
 132   vtkPolyData * mesh = mROI->GetMesh();
 133
 134   // Get bounds
 135   double *bounds=mesh->GetBounds();
 136   // for(int i=0; i<6; i++){
 137 //     DD(bounds[i]);
 138 //   }
 139
 140   // Compute origin
 141   std::vector<double> origin;
 142   origin.resize(3);
 143   origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
 144   origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
 145   origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
 146
 147   // Compute extend
 148   std::vector<double> extend;
 149   extend.resize(3);
 150   extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
 151   extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
 152   extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
 153
 154   // If no crop, set initial image size/origin
 155   if (!mCropMask) {
 156     for(int i=0; i<3; i++) {
 157       origin[i] = mOrigin[i];
 158       extend[i] = mSize[i]-1;
 159     }
 160   }
 161
 162   // Create new output image
 163   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
 164   mBinaryImage->SetScalarTypeToUnsignedChar();
 165   mBinaryImage->SetOrigin(&origin[0]);
 166   mBinaryImage->SetSpacing(&mSpacing[0]);
 167   mBinaryImage->SetExtent(0, extend[0],
 168                           0, extend[1],
 169                           0, extend[2]);
 170   mBinaryImage->AllocateScalars();
 171
 172   // for(int i=0; i<3; i++){
 173   //     DD(origin[i]);
 174   //     DD(extend[i]);
 175   //     DD(mBinaryImage->GetDimensions()[i]);
 176   //   }
 177   memset(mBinaryImage->GetScalarPointer(), 0,
 178          mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
 179
 180   // Extrude
 181   vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 182   extrude->SetInput(mesh);
 183   ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
 184   extrude->SetVector(0, 0, -mSpacing[2]);
 185
 186   // Binarization
 187   vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 188   //The following line is extremely important
 189   //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 190   sts->SetTolerance(0);
 191   sts->SetInformationInput(mBinaryImage);
 192   sts->SetInput(extrude->GetOutput());
 193   //sts->SetInput(mesh);
 194
 195   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 196   stencil->SetStencil(sts->GetOutput());
 197   stencil->SetInput(mBinaryImage);
 198   stencil->ReverseStencilOn();
 199   stencil->Update();
 200
 201   /*
 202   vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 203   w->SetInput(stencil->GetOutput());
 204   w->SetFileName("binary2.mhd");
 205   w->Write();
 206   */
 207
 208   mBinaryImage->ShallowCopy(stencil->GetOutput());
 209
 210   if (mWriteOutput) {
 211     typedef itk::Image<unsigned char, 3> ImageType;
 212     typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
 213     ConnectorType::Pointer connector = ConnectorType::New();
 214     connector->SetInput(GetOutput());
 215     connector->Update();
 216     clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
 217   }
 218 }
 219 //--------------------------------------------------------------------
 220
 221
 222
 223 //--------------------------------------------------------------------
 224 vtkImageData * clitk::DicomRTStruct2ImageFilter::GetOutput()
 225 {
 226   assert(mBinaryImage);
 227   return mBinaryImage;
 228 }
 229 //--------------------------------------------------------------------
 230